Decoding the Equine Genome: Lessons from ENCODE.
FAANG
epigenetics
functional annotation
gene regulation
health
horse
transcriptome
welfare
Journal
Genes
ISSN: 2073-4425
Titre abrégé: Genes (Basel)
Pays: Switzerland
ID NLM: 101551097
Informations de publication
Date de publication:
27 10 2021
27 10 2021
Historique:
received:
30
09
2021
revised:
24
10
2021
accepted:
26
10
2021
entrez:
27
11
2021
pubmed:
28
11
2021
medline:
16
2
2022
Statut:
epublish
Résumé
The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era.
Identifiants
pubmed: 34828313
pii: genes12111707
doi: 10.3390/genes12111707
pmc: PMC8625040
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Références
Exp Mol Med. 2017 Apr 28;49(4):e324
pubmed: 28450737
Mol Cell Biol. 1992 May;12(5):2424-31
pubmed: 1569958
Cell. 2008 Feb 8;132(3):422-33
pubmed: 18237772
Cell Mol Life Sci. 2016 Jul;73(13):2491-509
pubmed: 27007508
Genes (Basel). 2019 Dec 18;11(1):
pubmed: 31861495
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
NAR Genom Bioinform. 2021 Sep 03;3(3):lqab077
pubmed: 34514392
Sci Rep. 2020 Mar 23;10(1):5230
pubmed: 32251359
J Mol Biol. 1985 Sep 20;185(2):341-58
pubmed: 2997449
Cell Rep. 2013 May 30;3(5):1678-1689
pubmed: 23707059
Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6
pubmed: 21106759
Genome Biol. 2015 Aug 21;16:172
pubmed: 26294014
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Genome Biol. 2015 Mar 25;16:57
pubmed: 25854118
Genes (Basel). 2019 Jun 20;10(6):
pubmed: 31226862
Nature. 2020 Aug;584(7820):244-251
pubmed: 32728217
EMBO J. 1994 Apr 15;13(8):1823-30
pubmed: 8168481
Cell. 2015 Aug 13;162(4):900-10
pubmed: 26276636
Biotechnol Appl Biochem. 2021 Sep 22;:
pubmed: 34550619
Science. 2013 Oct 11;342(6155):253-7
pubmed: 24115442
Anim Genet. 2018 Dec;49(6):564-570
pubmed: 30311254
Neuroscientist. 2021 Oct 6;:10738584211046889
pubmed: 34612730
Cell Rep. 2016 May 31;15(9):2038-49
pubmed: 27210764
Subcell Biochem. 2007;41:319-36
pubmed: 17484134
Nat Rev Genet. 2006 Sep;7(9):703-13
pubmed: 16909129
Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63
pubmed: 24259432
Cytogenet Genome Res. 2009;126(1-2):165-72
pubmed: 20016166
Oncogene. 1990 Dec;5(12):1743-53
pubmed: 2284094
Nature. 2012 Sep 6;489(7414):101-8
pubmed: 22955620
Nucleic Acids Res. 2008 Sep;36(16):5221-31
pubmed: 18684996
Nat Rev Mol Cell Biol. 2003 Oct;4(10):809-14
pubmed: 14570061
Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7
pubmed: 19474294
Mol Cell. 2009 Jan 16;33(1):1-13
pubmed: 19150423
Front Genet. 2021 Jun 16;12:641788
pubmed: 34220931
Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6456-65
pubmed: 26499245
Nat Genet. 2004 Aug;36(8):900-5
pubmed: 15247917
Nat Biotechnol. 2021 Nov;39(11):1453-1465
pubmed: 34140680
Nat Rev Drug Discov. 2021 Aug;20(8):629-651
pubmed: 34145432
Oncogene. 2007 Aug 13;26(37):5310-8
pubmed: 17694074
Nature. 2020 Jul;583(7818):760-767
pubmed: 32728245
BMC Genomics. 2011 Jun 06;12:293
pubmed: 21645359
Cell. 2017 May 4;169(4):693-707.e14
pubmed: 28475897
Science. 2009 Nov 6;326(5954):865-7
pubmed: 19892987
Cell. 2006 Apr 21;125(2):315-26
pubmed: 16630819
Cell. 2002 Dec 13;111(6):771-8
pubmed: 12526804
Front Genet. 2021 Mar 26;12:649959
pubmed: 33841506
Genome Res. 2011 Oct;21(10):1757-67
pubmed: 21750106
Nucleic Acids Res. 2021 Jan 8;49(D1):D884-D891
pubmed: 33137190
Nature. 2020 Jul;583(7818):699-710
pubmed: 32728249
Proc Natl Acad Sci U S A. 1964 May;51:786-94
pubmed: 14172992
Mol Cell Biol. 1996 Jun;16(6):2802-13
pubmed: 8649389
Nat Biotechnol. 2015 Nov;33(11):1165-72
pubmed: 26458175
Epigenetics Chromatin. 2015 Jan 13;8:2
pubmed: 25788983
Nat Biotechnol. 2010 Aug;28(8):817-25
pubmed: 20657582
Genome Res. 2006 Jan;16(1):123-31
pubmed: 16344561
Trends Genet. 2015 May;31(5):239-51
pubmed: 25869999
Science. 2014 Jun 20;344(6190):1396-401
pubmed: 24925914
Am J Hum Genet. 2014 Nov 6;95(5):535-52
pubmed: 25439723
Annu Rev Genet. 2015;49:673-95
pubmed: 26631517
Chromosoma. 2015 Jun;124(2):277-87
pubmed: 25413176
Curr Protoc Mol Biol. 2015 Jan 05;109:21.29.1-21.29.9
pubmed: 25559105
Mol Ther Nucleic Acids. 2021 Oct 08;26:828-848
pubmed: 34729251
PLoS Genet. 2020 Sep 28;16(9):e1009028
pubmed: 32986719
Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20398-403
pubmed: 19074263
Nature. 2012 Sep 6;489(7414):75-82
pubmed: 22955617
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Sci Rep. 2019 Nov 1;9(1):15800
pubmed: 31676881
Cell. 2013 Aug 15;154(4):888-903
pubmed: 23953118
Cell. 2007 May 18;129(4):823-37
pubmed: 17512414
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Am J Hum Genet. 2013 Nov 7;93(5):779-97
pubmed: 24210251
Genetics. 1993 Aug;134(4):1135-44
pubmed: 8375652
Front Genet. 2021 Mar 08;12:650305
pubmed: 33763124
Genome Biol. 2016 Feb 04;17:20
pubmed: 26846207
EMBO J. 2008 Nov 5;27(21):2839-50
pubmed: 18923423
Nat Methods. 2012 Feb 28;9(3):215-6
pubmed: 22373907
J Biol Chem. 1997 Dec 26;272(52):33353-9
pubmed: 9407128
Anim Genet. 2019 Dec;50(6):569-597
pubmed: 31568563
Prog Mol Subcell Biol. 2017;56:337-354
pubmed: 28840244
Genome Res. 2012 Sep;22(9):1711-22
pubmed: 22955983
BMC Genomics. 2020 Oct 7;21(1):698
pubmed: 33028202
Nat Genet. 2007 Mar;39(3):311-8
pubmed: 17277777
Genome Res. 2018 Jun;28(6):789-799
pubmed: 29712753
Trends Genet. 2001 Sep;17(9):520-7
pubmed: 11525835
Nat Genet. 2009 Aug;41(8):885-90
pubmed: 19561604
Nucleic Acids Res. 2019 Jan 8;47(D1):D766-D773
pubmed: 30357393
Equine Vet J. 2021 Mar;53(2):316-323
pubmed: 32654228
Cell. 2015 Aug 13;162(4):703-5
pubmed: 26276625
Nature. 2000 Jan 6;403(6765):41-5
pubmed: 10638745
Commun Biol. 2018 Nov 16;1:197
pubmed: 30456315
Genes Dev. 2006 Sep 1;20(17):2349-54
pubmed: 16951251
BMC Genomics. 2020 Nov 30;21(1):848
pubmed: 33256610
PLoS Comput Biol. 2008 Oct;4(10):e1000201
pubmed: 18927605
Science. 2012 Sep 7;337(6099):1190-5
pubmed: 22955828
Nature. 2008 Feb 14;451(7180):796-801
pubmed: 18235444
Nature. 2006 May 18;441(7091):349-53
pubmed: 16625203
Nature. 2013 Oct 3;502(7469):59-64
pubmed: 24067610
Cell. 1990 May 4;61(3):505-14
pubmed: 2159385
Nat Genet. 2018 Aug;50(8):1151-1160
pubmed: 29988121
Cell. 2007 Mar 23;128(6):1231-45
pubmed: 17382889
Cell Rep. 2015 Mar 3;10(8):1297-309
pubmed: 25732821
Nature. 1997 Sep 18;389(6648):251-60
pubmed: 9305837
Nat Methods. 2017 Oct;14(10):959-962
pubmed: 28846090
Mol Cell Biol. 2010 Mar;30(6):1411-20
pubmed: 20065031
Nat Cell Biol. 2013 Sep;15(9):1056-66
pubmed: 23873148
Nature. 2010 Aug 5;466(7307):714-9
pubmed: 20686566
Cell. 1987 Apr 24;49(2):203-10
pubmed: 3568125
Nat Immunol. 2014 Jun;15(6):484-91
pubmed: 24840979
Science. 2004 Oct 22;306(5696):636-40
pubmed: 15499007
J Clin Invest. 2016 Nov 1;126(11):4205-4218
pubmed: 27760051
Cell. 1999 Aug 6;98(3):387-96
pubmed: 10458613
Animals (Basel). 2020 Jun 04;10(6):
pubmed: 32512843
Science. 1974 May 24;184(4139):868-71
pubmed: 4825889
PLoS Genet. 2010 Feb 12;6(2):e1000845
pubmed: 20169180
Genomics. 2006 Jun;87(6):777-82
pubmed: 16413164
Proc Natl Acad Sci U S A. 2004 May 11;101(19):7357-62
pubmed: 15123803
Mol Cell. 2014 Mar 20;53(6):1005-19
pubmed: 24530304
Cell. 2008 Jan 25;132(2):311-22
pubmed: 18243105